Installation

https://github.com/Genome3d/codes3d.gitcd codes3d/

Setup

sudo apt updatesudo apt install -y libz-dev libxslt1-dev libpq-dev python3-pip python3-dev python3-virtualenv bedtoolspip3 install --upgrade pip virtualenv setuptools

Create environment with conda

conda env create --prefix ./codes3d_env --file environment.yaml

conda activate codes3d_env/

conda deactivate

Data installation

Basic Usage

(/mnt/projects/codes3d/codes3d_env) /m/p/codes3d$ python codes3d/codes3d.py -husage: codes3d.py [-h] [-s SNP_INPUT [SNP_INPUT ...]] [-g GENE_INPUT [GENE_INPUT ...]] [--snps-within-gene SNPS_WITHIN_GENE [SNPS_WITHIN_GENE ...]] [-o OUTPUT_DIR] [--multi-test MULTI_TEST] [--pval-threshold PVAL_THRESHOLD]                  [-f FDR_THRESHOLD] [--maf-threshold MAF_THRESHOLD] [-p NUM_PROCESSES] [--no-afc] [--afc-bootstrap AFC_BOOTSTRAP] [-n INCLUDE_CELL_LINES [INCLUDE_CELL_LINES ...]] [-x EXCLUDE_CELL_LINES [EXCLUDE_CELL_LINES ...]]                  [--list-hic-libraries] [--match-tissues ...] [--list-tissue-tags] [-t TISSUES [TISSUES ...]] [--eqtl-project EQTL_PROJECT] [--list-eqtl-db] [-r RESTRICTION_ENZYMES [RESTRICTION_ENZYMES ...]] [--list-enzymes]                  [--list-eqtl-tissues] [-c CONFIG] [--output-format OUTPUT_FORMAT] [--do-not-produce-summary] [--suppress-intermediate-files] [--non-spatial] [--gene-list GENE_LIST [GENE_LIST ...]] [--gtex-cis]CoDeS3D maps gene regulatory landscape using chromatin        interaction and eQTL data.optional arguments:  -h, --help            show this help message and exit  -s SNP_INPUT [SNP_INPUT ...], --snp-input SNP_INPUT [SNP_INPUT ...]                        The dbSNP IDs or loci of SNPs of interest in the format 'chr<x>:<locus>'. Use this flag to identify eGenes associated with the SNPs of interest.  -g GENE_INPUT [GENE_INPUT ...], --gene-input GENE_INPUT [GENE_INPUT ...]                        The symbols, Ensembl IDs or loci of genes interest in the format 'chr<x>:<start>-<end>'. Use this flag to identify eQTLs associated with the gene of interest.  --snps-within-gene SNPS_WITHIN_GENE [SNPS_WITHIN_GENE ...]                        A gene symbol, Ensembl ID or location in the format 'chr<x>:<start>-<end>'. Use this flag to identify eGenes associated with the SNPs located within the gene of interest.  -o OUTPUT_DIR, --output-dir OUTPUT_DIR                        The directory in which to output results.  --multi-test MULTI_TEST                        Options for BH multiple-testing: ['snp', 'tissue', 'multi']. 'snp': corrects for genes associated with a given SNP in a given tissue. 'tissue': corrects for all associations in a given tissue. 'multi': corrects                        for all associations across all tissues tested.  --pval-threshold PVAL_THRESHOLD                        Maximum p value for mapping eQTLs. Default: 1.  -f FDR_THRESHOLD, --fdr-threshold FDR_THRESHOLD                        The FDR threshold to consider an eQTL statistically significant (default: 0.05).  --maf-threshold MAF_THRESHOLD                        Minimum MAF for variants to include. Default: 0.1.  -p NUM_PROCESSES, --num-processes NUM_PROCESSES                        Number of CPUs to use (default: half the number of CPUs).  --no-afc              Do not calculate allelic fold change (aFC). If true, eQTL beta (normalised effect size) is calculated instead. (default: False).  --afc-bootstrap AFC_BOOTSTRAP                        Number of bootstrap for aFC calculation (default: 1000).  -n INCLUDE_CELL_LINES [INCLUDE_CELL_LINES ...], --include-cell-lines INCLUDE_CELL_LINES [INCLUDE_CELL_LINES ...]                        Space-separated list of cell lines to include (others will be ignored). NOTE: Mutually exclusive with EXCLUDE_CELL_LINES. --match-tissues takes precedence.  -x EXCLUDE_CELL_LINES [EXCLUDE_CELL_LINES ...], --exclude-cell-lines EXCLUDE_CELL_LINES [EXCLUDE_CELL_LINES ...]                        Space-separated list of cell lines to exclude (others will be included). NOTE: Mutually exclusive with INCLUDE_CELL_LINES. --match-tissues and -n take precedence.  --list-hic-libraries  List available Hi-C libraries.  --match-tissues ...   Try to match eQTL and Hi-C tissue types using space-separated tags. When using this, make sure that it is the last tag. Note that tags are combined with the AND logic. Prepend "-" to a tag if you want it to be                        excluded. Use `--list-tissues-tags' for possible tags.  --list-tissue-tags    List tags to be used with `--match-tissues'.  -t TISSUES [TISSUES ...], --tissues TISSUES [TISSUES ...]                        Space-separated list of eQTL tissues to query. Note that tissues are case-sensitive and must be from the same eQTL projects. Default is all tissues from the GTEx project. Use 'codes3d.py --list-eqtl-tissues'                        for a list of installed tissues.  --eqtl-project EQTL_PROJECT                        The eQTL project to query. Default: GTEx. 'use 'codes3d.py --list-eqtl-db' to list available databases.  --list-eqtl-db        List available eQTL projects to query.  -r RESTRICTION_ENZYMES [RESTRICTION_ENZYMES ...], --restriction-enzymes RESTRICTION_ENZYMES [RESTRICTION_ENZYMES ...]                        Space-separated list of restriction enzymes used in Hi-C data.' Use 'list-enzymes' to see available enzymes.  --list-enzymes        List restriction enzymes used to prepare installed Hi-C libraries.  --list-eqtl-tissues   List available eQTL tissues to query.  -c CONFIG, --config CONFIG                        The configuration file to use (default: docs/codes3d.conf).  --output-format OUTPUT_FORMAT                        Determines columns of output. 'short': snp|gencode_id|gene|tissue|adj_pval| [log2_aFC|log2_aFC_lower|log2_aFC_upper] or [beta|beta_se]| maf|interaction_type|hic_score. 'medium' adds:                        eqtl_pval|snp_chr|snp_locus|ref|alt|gene_chr| gene_start|gene_end|distance. 'long' adds:cell_lines|cell_line_hic_scores| expression|max_expressed_tissue|max_expression| min_expressed_tissue|min_expression.                        (default: long).  --do-not-produce-summary                        Do not produce final summary file, stop process after mapping eQTLs. Helpful if running batches (default: False).  --suppress-intermediate-files                        Do not produce intermediate files. These can be used to run the pipeline from an intermediate stage in the event of interruption (default: False).  --non-spatial         Map non-spatial eQTLs.  --gene-list GENE_LIST [GENE_LIST ...]                        List of genes for non-spatial eQTL mapping.  --gtex-cis            Retrieve spatially unconstrained cis-eQTLs as calculated in GTEx. To be used in combination with 'non-spatial'.

export PATH=$PATH:/path/to/CoDeS3D # Replace "/path/to" with the path where the CoDeS3D program is stored

cd /usr/local/binsudo ln -s /path/to/CoDeS3D CoDeS3D # Replace "/path/to" with the path where the CoDeS3D program is stored